Hi!
I just wanted to do a test run with Tophat2 but it appears more difficult than anticipated...
So I installed SAMtools and Bowtie2 in the required versions and then used the "make_hg19.sh" script from Bowtie to get the hg19 indexes. So far so good. But now when I run Tophat2 I get this:
So it doesn't recognize the fasta files in that folder. Possibly because these are by chromosome and do not carry the same name as the index files. Eitherway Tophat2 should be able to reconstruct the fasta file from the index. Can anyone tell me where I went wrong?
I just wanted to do a test run with Tophat2 but it appears more difficult than anticipated...
So I installed SAMtools and Bowtie2 in the required versions and then used the "make_hg19.sh" script from Bowtie to get the hg19 indexes. So far so good. But now when I run Tophat2 I get this:
Code:
tophat2 /usr/bin/bowtie2-2.2.2/indexes/hg19 FASTQ11_1.fq FASTQ12_2.fq [2014-05-23 09:56:35] Beginning TopHat run (v2.0.11) ----------------------------------------------- [2014-05-23 09:56:35] Checking for Bowtie Bowtie version: 2.2.2.0 [2014-05-23 09:56:35] Checking for Samtools Samtools version: 0.1.18.0 [2014-05-23 09:56:35] Checking for Bowtie index files (genome).. [2014-05-23 09:56:35] Checking for reference FASTA file Warning: Could not find FASTA file /usr/bin/bowtie2-2.2.2/indexes/hg19.fa [2014-05-23 09:56:35] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie2-2.2.2/bowtie2-inspect /usr/bin/bowtie2-2.2.2/indexes/hg19 > ./tophat_out/tmp/hg19.fa [FAILED] Error: bowtie-inspect returned an error bowtie-inspect: reference.cpp:471: int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t, SStringExpandable<unsigned int, 1024, 2>&) const: Assertion `0' failed.
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